NovoPlasty is producing identical Assemblies

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5.7 years ago

micro32uvas ▴ 10

Hello,

I have been extracting the mitochondria from my whole genome sequence data. This one sample, produced 3 assemblies, 2 of them are identical and the third one is close to the validated sequence (I did sanger to compare)

It is seed and extend based and I cannot understand why it produced exact same assemblies twice in a single run. the contig size, insert size are all same

Thanks,

Novoplasty Assembly mitochondria • 2.2k views

ADD COMMENT • link updated 5.5 years ago by Biostar 20 • written 5.7 years ago by micro32uvas ▴ 10

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What do you mean by this?

This one sample, produced 3 assemblies

I am not questioning the tool, however, be careful with the results. There are known issues here

ADD REPLY • link 5.5 years ago by lakhujanivijay 5.8k

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Yeah and to combat this issue, I went with Sanger for the confirmation. Turned out there was read depth problem at some locations, in case of multiple assemblies. They didn't vary much but few of them made multiple. Ruled the problem out by Sanger.

ADD REPLY • link 5.5 years ago by micro32uvas ▴ 10

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Fantastic. I rarely rely on tools which produce a single contig. Validations must follow

ADD REPLY • link 5.5 years ago by lakhujanivijay 5.8k

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